<tool id="tepid_merge_insertions" name="tepid-merge-insertions" version="@WRAPPER_VERSION@">
    <description>discover TE variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>tepid-discover --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #for $input in $insertions:
            ln -s -f '$input' '$input.element_identifier' &&
        #end for
        python '$__tool_directory__'/merge_insertions.py -i
        #for $input in $insertions:
            '$input.element_identifier'
        #end for
        -o '$merged_out'
    ]]></command>
    <inputs>
        <param name="insertions" label="TEPID insertions" argument="--input" type="data_collection" format="bed"/>
    </inputs>
    <outputs>
        <data name="merged_out" format="bed" label="tepid_discover merged insertions on ${on_string}">
        </data>
    </outputs>
    <tests>
        <test>
      <param name="insertions">
          <collection type="list">
              <element name="1" value="1.bed" />
              <element name="2" value="2.bed" />
          </collection>
        </param>
           <output name="merged_out" file="test.bed"/>
        </test>
    </tests>
    <help><![CDATA[
        This step merges insertions found by tepid discover.
        The output can be used as input in the tepid-refine step.
    ]]></help>
<expand macro="citations"/>
</tool>